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CLINE

CLINE (Comparison of bioLogIcal deNdrogram structurEs), is a web-tool specifically designed for the visual comparison of dendrograms, with an emphasis on the display of matching clusters that, even when not isomorphic, can be perceived as having the same biological meaning.

The comparison of dendrograms is available at three different levels: Bio-Isomorphic, Re-arrangement and Containment.

To define these levels, let us consider the clustering of an experiment containing a series of biological replicates, such as the one shown in Fig. 1. It compares paired, clustered samples of the Iris dataset, each containing at most 5 replicates of Iris Setosa.

1. Bio-Isomorphic: Matches clusters that have the same structure in the same position on both dendrograms, except for a possible permutation of the replicates. The number of nodes and the structure of the branches are retained in both matching clusters (Fig. 1a).

2. Re-arrangement: Matches clusters that consist of identical sets of nodes even if the branches from the root of the cluster to the leaves are different (Fig. 1b).

3. Containment: Matches clusters in which the set of nodes in one cluster is a proper subset of the other (Fig. 1c).

Figure 1: Cluster matching using the three levels of similarity implemented in our application. (a) Both clusters considered equivalent, even when replicates 2 and 4 are on different branches. (b) Clusters are equivalent, even if the organization of the branches is different. (c) Clusters are equivalent, even when one of them has a smaller number of replicates. Equal branches within matched clusters are also highlighted.